DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s election without traverse of Group I, claims 1-2, 6-13, 19-25, 27, 30-32, 34, 37-38, and 106 drawn to a host cell comprising from 1-500 integrated docking sites with at least one dock site insertion element in the reply filed on 01/07/2026 is acknowledged.
Claims 108, 113, and 133 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected inventions, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 01/07/2026.
Priority
Acknowledgement is made of Applicants’ claim for benefit to prior filed US Provisional Applications 63033516 and 63033514, filed on 06/02/2020.
This application claims the benefit of priority to Patent Application PCT/US2021/035403. Acknowledgement is made of Applicants’ claim for benefit to prior filed to Patent Application Number PCT/US2021/035403, filed on 06/02/2021.
Information Disclosure Statement
The Information Disclosure Statements filed 11/05/2025, 02/10/2026, 09/26/2025, 11/15/2024, 03/14/2023 have been considered by the Examiner.
Status of Claims
Claims 1-2, 6-13, 19-25, 27, 30-32, 34, 37-38, and 106 are under examination.
Claims 108, 113, and 133 are withdrawn.
Claims 3-5, 14-18, 26, 28-29, 33, 35-36, 39-105, 107, 109-112, 114-132, and 134-184 are cancelled.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-2, 6-9, 12-13, 19-25, 27, 30-32, 34, and 106 are rejected under 35 U.S.C. 102 (a)(1) as being anticipated by Fahrenkrug et al. (US20180235194).
Regarding claim 1, Fahrenkrug et al. teach multiple gene edits in a cell or embryo. Fahrenkrug et al. teach the gene edits comprise a first targeted endonuclease directed to a first target chromosomal DNA site and a first homology directed repair (HDR) template that has homology to the first target chromosomal DNA site, wherein the first HDR template replaces the first target chromosomal DNA site. Fahrenkrug et al. teach the gene edits further comprise a second targeted endonuclease directed to a second target chromosomal DNA site and a second HDR template that has homology to the second target chromosomal DNA site wherein the second HDR template replaces the second target chromosomal DNA site (page 32&page 9, claim 25, paragraph 0069).The template may further comprise flanking sequences that provide homology to DNA adjacent to the endogenous allele or the DNA that is to be replaced. The docking site insertion element of Fahrenkrug is the HDR template. As described, Fahrenkrug et al. teach a host cell comprising a genome, the genome comprising multiple integrated docking sites, each docking site comprising at least one dock site insertion element.
Regarding claim 2, Fahrenkrug et al. teach seven targeted endonucleases directed to a seven chromosomal DNA sites and a seven HDR templates that have homology to the seven target chromosomal DNA sites wherein the HDR templates replace the target chromosomal DNA site (page 33, claims 25 and 28). As described, Fahrenkrug et al. teach a host cell wherein the genome comprises 5-7 docking sites each docking site comprising at least one dock site insertion element.
Regarding claim 6, Fahrenkrug et al. teach the integrated docking sites are independently positioned throughout the genome (page 33, claims 25 and 28).
Regarding claim 7, Fahrenkrug et al. teach a TAL effector target can be used to target other protein domains to specific nucleotide sequences. Fahrenkrug et al. teach a TAL effector can be linked to a protein domain, an interacting enzyme an integrase (page 10, paragraph 0072).
Regarding claim 8, Fahrenkrug et al. teach the sequence encoding a selectable marker can be flanked by recognition sequences for a recombinase (page 11, paragraph 0084). Fahrenkrug et al. teach a recombinase may be combined with a nucleic acid sequence that serves
as a template for HDR (page 15, paragraph 0115).
Regarding claim 9, Fahrenkrug et al. teach a recombinase may be combined with a nucleic acid sequence that serves as a template for HDR (page 15, paragraph 0115).
Regarding claim 12, Fahrenkrug et al. teach a sequence encoding a selectable marker can be flanked by recognition sequences for a Cre recombinase. Fahrenkrug et al. teach the selectable marker can be flanked by loxP recognition sites (page 11, paragraph 0085).
Regarding claim 13, Fahrenkrug et al. teach the selectable marker can be flanked by FRT recognition sites (page 11, paragraph 0085).
Regarding claim 19, Fahrenkrug et al. teach nucleic acids incorporated into vectors. Fahrenkrug et al. teach the transcriptional unit of a nucleic acid construct, the regulatory region operably linked to an exogenous nucleic acid sequence (page 12, paragraphs 0087-0088).
Regarding claim 20, Fahrenkrug et al. teach an exogenous integrating vector where the sequence is selected from viral vectors and transposons (page 12, paragraph 0089).
Regarding claim 21, Fahrenkrug et al. teach a sequence encoding a selectable marker can be flanked by recognition sequences for a Cre recombinase. Fahrenkrug et al. teach the selectable marker can be flanked by loxP recognition sites (34-bp recognition sites recognized by the Cre recombinase) or FRT recognition sites such that the selectable marker can be excised from the construct. Fahrenkrug et al. teach a transposon containing a Cre- or Flp-activatable transgene interrupted by a selectable marker gene also can be used to obtain transgenic animals with conditional expression of a transgene. Fahrenkrug et al. further teach a promoter driving expression (page 11, paragraphs 0084-0085).
Regarding claim 22, Fahrenkrug et al. teach the target nucleic acid sequence can be operably linked to a regulatory region such as a promoter (page 11, paragraph 0081). Fahrenkrug et al. teach the transcriptional unit of a nucleic acid construct, where the regulatory region operably linked to an exogenous nucleic acid sequence (page 12, paragraph 0087). Fahrenkrug et al. teach Cre recombinase is an enzyme (page 16, paragraph 0116). Fahrenkrug et al. teach the tetracycline-inducible system and the Cre/loxP recombinase system are inducible systems (page 14, paragraph 0108).
Regarding claim 23, Fahrenkrug et al. teach exogenous nucleic acid that is either inserted into the chromosome for repair of the break in a cell with a modified sequence. Fahrenkrug et al. teach the tetracycline-inducible system and the Cre/loxP recombinase system are inducible systems (page 14, paragraph 0108).
Regarding claim 24, Fahrenkrug et al. teach the target nucleic acid sequence can be operably linked to a regulatory region such as a promoter (page 11, paragraph 0081). Fahrenkrug et al. teach the target nucleic acid sequence can be operably linked to a regulatory region such as a promoter (page 11, paragraph 0080).
Regarding claim 25, Fahrenkrug et al. teach is a broad term that includes any specific DNA segment that is designed to move from a carrier into a target DNA. Fahrenkrug et al. teach the vector may be an episomal expression vector (page 12, paragraph 0089).
Regarding claim 27, Fahrenkrug et al. teach a Cas9 nuclease was provided by co-transfection of the hCas9 plasmid (page 20, paragraph 0136). Fahrenkrug et al. teach a vector comprised of DNA and a transposase, recombinase, or other integrase enzyme that recognizes both the vector and a DNA target sequence and inserts the vector into the target DNA sequence (page 12, paragraph 0089).
Regarding claims 30 and 31, Fahrenkrug et al. teach introducing multiple gene edits in a cell or embryo comprising simultaneously introducing into a cell a second targeted endonuclease directed to a second target chromosomal DNA site and a second HDR template that has homology to the second target chromosomal DNA site a first targeted endonuclease directed to a first target chromosomal DNA site and a first homology directed repair (HDR) template that has homology to the first target chromosomal DNA site; and wherein the first HDR template replaces the first target chromosomal DNA site and the second HDR template replaces the second target chromosomal DNA site (page 32, claim 25). Fahrenkrug et al. further teach crossover between two distant Cre recognition sequences, loxP sites for recognition and cassette exchange (page 15, paragraph 0110).
Regarding claim 34, Fahrenkrug et al. teach multiple gene edits in a cell or embryo comprising a first targeted endonuclease directed to a first target chromosomal DNA site and a first homology directed repair (HDR) template that has homology to the first target chromosomal DNA site, wherein the first HDR template replaces the first target chromosomal DNA site. Fahrenkrug et al. further teach a second targeted endonuclease directed to a second target chromosomal DNA site and a second HDR template that has homology to the second target chromosomal DNA site wherein the second HDR template replaces the second target chromosomal DNA site (pages 9 and 32, paragraph 0069 and claim 25). The docking site insertion element of Fahrenkrug is the HDR template. Fahrenkrug et al. further teach vertebrate animal chimeric for host cells and donor cells comprising a plurality of host cell genetic edits at different chromosomal DNA sites, and a donor cell integrated with the host cells to form the chimeric animal (page 24, paragraph 0204).
Regarding claim 106, Fahrenkrug et al. teach cells were cultured so that they formed individual colonies of cells (page 4, paragraph 0036).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 10 and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Fahrenkrug et al. (US20180235194). as applied to claims 1,8, and 9 above, and further in view of Merrick et al. (ACS Synthetic Biology, 2018).
Fahrenkrug et al. teach a host cell comprising a genome, the genome with multiple integrated docking sites, each docking site comprising at least one dock site insertion element.
Regarding claim 10, Fahrenkrug et al. teach a TAL effector can be linked to a protein domain, an interacting enzyme an integrase (page 10, paragraph 0072). Fahrenkrug et al. teach a vector comprised of DNA and a transposase, recombinase, or other integrase enzyme that recognizes both the vector and a DNA target sequence and inserts the vector into the target DNA sequence (page 12, paragraph 0089).
Fahrenkrug et al. do not teach dock site insertion element comprises an attachment site (att).
Merrick et al. teach serine integrases are encoded by temperate bacteriophages and catalyze their integration into bacterial genomes through recombination of attP (phage) and attB (bacteria) attachment sites (page 299, Serine Integrase Site-Specific Recombination). Merrick et al. teach serine integrases, and their cognate RDFs and att sites, provide reliable DNA recombination systems that can be used in a number of applications including in vivo genomic integration of DNA in a range of organisms, and in vitro assembly and targeted modification of DNA constructs (page 307, Prospects for Serine Integrases). Merrick et al. teach compared to transcription-based biological logic and memory systems including those that use CRISPR-Cas9 components, serine integrase-based devices have a simple composition comprising of DNA, integrases and RDFs. Merrick et al. teach serine integrases and RDFs are active in a range of cell-types and do not rely on endogenous DNA repair systems for DNA modification, these devices could be made portable and utilized in multiple organisms. Merrick et al. teach data stored in DNA can be reliably retained throughout cell divisions, transferred across species, and easily detected after cell death. Merrick et al. teach the devices have the potential to detect transient signals and to record data in otherwise inaccessible environments (page 306, Serine Integrase Logic and Memory Devices).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to have combined the teachings of Fahrenkrug et al. for a host cell comprising a genome, the genome with multiple integrated docking sites, each docking site comprising at least one dock site insertion element with the teachings of Merrick et al. for teach serine integrases are encoded by temperate bacteriophages. Merrick et al. provide motivation by teaching that Merrick et al. provide motivation by teaching that serine integrases, and their cognate RDFs and att sites, provide reliable DNA recombination systems that can be used in a number of applications including in vivo genomic integration of DNA in a range of organisms, and in vitro assembly and targeted modification of DNA constructs. One of skill in the art would have had a reasonable expectation of success at combining Fahrenkrug et al. and Merrick et al. because both teach bacteriophage as a vector cell genome modification.
Regarding claim 11, Merrick et al. teach serine integrases are encoded by temperate bacteriophages and catalyze their integration into bacterial genomes through recombination of attP (phage) and attB (bacteria) attachment sites, generating attL (left) and attR (right) sites (page 299, Serine Integrase Site-Specific Recombination). Merrick et al. teach recombination of attP and attB is highly directional, it is not reversible in the presence of the serine integrase alone (page 299, Serine Integrase Site-Specific Recombination).
Claims 37 and 38 are rejected under 35 U.S.C. 103 as being unpatentable over Fahrenkrug et al. (US20180235194). as applied to claims 1 and 34 above.
Regarding claims 37 and 38, Fahrenkrug et al. teach mammalian expression plasmids typically have an origin of replication, a suitable promoter and optional enhancer, and also any necessary ribosome binding sites, a polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5' flanking non-transcribed sequences (page 12, paragraph 0090). Fahrenkrug et al. teach a first promoter sequence; a selectable marker sequence; a second promoter sequence; a nucleic acid sequence encoding a first protein of interest that is operably linked to the internal promoter; and a poly A signal sequence. One of ordinary skill in the art would be experienced in vector design and is well equipped to order the components of the vector as described by Fahrenkrug et al.
Conclusion
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/C.L.M./Examiner, Art Unit 1638
/Anna Skibinsky/
Primary Examiner, AU 1635
Prosecution Insights